Star Wars: The Clone Wars - Emergence The Red Sith Saga, Part One
by OrangeGalen
Summary: The Separatists have staged several brilliant offensives, capturing several systems. Obi-Wan Kenobi and Anakin Skywalker are tasked with recapturing the Bothan system, but things take a turn for the worse as a trap that has been set by a mysterious commander is sprung and both Jedi find themselves facing an unexpected deadly foe that could change the fate of the Clone Wars.
1. Prologue

This story is not cannon with the Star Wars franchise, but tries to stay close to the existing cannon (Wookipedia is a mess right now). I am a fan of the Clone Wars CGI show and this story has been in the works since season 2. I have recently dug it up and updated it for the end of season 5. This part takes place in-between the episodes "Tipping Points" and "The Gathering" of season 5. Around 20BBY.

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A crushing string of defeats! After several conflicts in the mid rim, the Separatists have dealt a grievous blow to the Republic by capturing several key systems including the Bothan sector. Now in control of the newly built Bothan shipyards, the Separatists will soon be able to build new warships to turn against the Republic, something that the Republic cannot afford. Anakin Skywalker and Obi-Wan Kenobi are sent to combat the fleet surrounding the planet Bothawui, so Master Luminara Unduli can land on the surface and recapture the system to prevent a devastating fleet from being constructed….


	2. Chapter 1- Invasion Plans

Anakin Skywalker always preferred to be in the cockpit of a star fighter rather than on a bridge of a Star Destroyer. Dodging laser blasts and enemy fighters in his Delta-7B _Aethersprite_ Interceptor was one of the more exciting things about combat and where he felt he could change the course of the battle. However, the Jedi Order had been losing far too many Jedi over the course of the war and clone pilots were some of the finest in the galaxy, so Anakin was stuck on the bridge of the _Dauntless_ with his own padawan Ahsoka Tano.

The _Dauntless_, along with the _Firebird_ and the _Adamant_, were three of the cruisers in the Bothan operation. Their mission was to destroy or at least occupy the attention of the Separatist fleet so the rest of the Republic fleet, led by general Obi-Wan Kenobi, could retake the shipyards. They would rejoin the fleet soon after that battle started to aid them. General Luminara Unduli would land after the space battle with the ground force to combat the Separatist forces down on the planet. Anakin recalled that the Bothans eventually decided to ally with the Republic after the attempted Separatist invasion led by General Grievous. That invasion was foiled by an ingenious plan led by himself involving AT-TE walkers deployed on the asteroids surrounding the gas giant Golm to ambush the Confederate ships as they entered range.

After that battle, the Bothans saw that neutrality was not a sustainable goal for them and voted to end their neutrality over the personal preference of their senator, Polo Se'lab. They had also constructed their own shipyards to aid the Republic, although they requested that the shipyards only have Bothan personal. But now that time had passed and they were under Separatist control. Now Anakin has returned to protect the Bothans once again.

Anakin was broken out of his thoughts by the sound of his padawan's voice, "We're coming up on the Bothan system."

"Then let's get ready." He turned from the viewport and looked at Ahsoka. "Tell the fighters to prep for launch, and also tell Odd Ball he'll have to manage without me this time."

"I'm sure he'll do just fine without you." Ahsoka responded. "I'll patch you in to Master Kenobi so you can update him on our status."

Anakin nodded and Ahsoka tapped some controls. Soon, a near life size hologram of Obi-Wan was in front of Anakin. With his trademark business bluntness Obi-wan said "_Report_."

"We're inbound to Bothawui and should be arriving momentarily Master." Anakin always added "Master" not just because Obi-Wan was a member of the Jedi council, but also of the age-old habit of when he was an apprentice.

_"Good, my fleet is also inbound and should arrive shortly after yours to give the Separatists a chance to intercept your force before we strike."_

"Let's hope they like the bait we offer them." Anakin said jokingly.

_"Yes,"_ Obi-wan mused, _" the CIS should be rather keen on keeping these shipyards. Even smaller ones like this one can tip the war in either side's favor."_

"Well, lets do some tipping in our favor, Master." Ahsoka chimed in, walking to face the holo.

Obi-Wan's projection smirked, _"Quite right Ahsoka. Anakin, keep comm channels open in case any situations arise."_

"Of course Master." Anakin replied.

_"Oh, and do try to keep your ships in one piece this time will you?"_

"What do you mean 'this time'?" Anakin said with a hint of feigned ignorance.

Ahsoka glanced at her screen and interrupted "One minute till we drop out of hyperspace."

_"Very well. I'll leave you two at it. Kenobi out."_ And with that, the hologram disappeared back into the table as the projectors died down.

Anakin walked around the table and, crossing his arms, stared out of the viewport into hyperspace. The final moments ticked away before reentry into normal space. The clone crew was making last minute adjustments to their stations and giving orders to other clones. Anakin was in the center of it, giving off a firm aura of calm and determination. "The Hero with No Fear" as the holonet was fond of calling Skywalker. He had risked his life countless times to save the people under his command and defied the odds so often many considered it to be second nature. Now he was out to crush another Separatist force and bring this ever-growing war another victory closer to ending.

Ahsoka, from her position in the comm area had a clear view of Anakin. She never grew tired of how he could appear to be so calm yet always be ready to burst into action at a second's notice. Over the years that she has been his apprentice, she had grown to realize that Skywalker was a man of action. And that action usually resulted in a sizeable pile of scrap metal during battles. But she always had the feeling that Anakin was holding something back, and on the rare occasion it did slip. But those instances were very few and far apart. She understood and had figured it was just the individual Jedi's personality. Some Jedi, like Kit Fisto and Aayla Secura sometimes let their emotions out while others like the stoic Mace Windu kept them on a tight leash. Obi-wan Kenobi, Ahsoka had figured, was in the middle of the two ranges, neither completely detached nor emotionally involved. _The right balance,_ she thought. However, being around Skywalker for so long has had an influence on her and now she leans more to the emotional side. She didn't mind however, she liked it that way. She glanced at the chronometer on the screen, showing ten seconds left before reentry. "Ten seconds left." She announced. _Time to get to work_.


	3. Chapter 2- The Trap Has Sprung

The streaks of hyperspace faded into the blackness of space. Ahead of the _Dauntless_ lay the small glowing speck that was the planet Bothawui. Close by loomed Golm, its asteroid ring forming a giant disk in space. Anakin turned to Ahsoka and said "Any signs of Separatist activity?"

"Scanning." She replied. The results were puzzling. "I'm not detecting any Separatist ships between us and the planet."

"What?" Anakin said as he came over to look at the readings. "That doesn't make any sense." He muttered. Ships should be forming a blockade formation around the planet to protect it from invasion. "Expand your scans to the cover the entire system."

Ahsoka responded and widened the scans. "There does seem to be a large buildup of Confederate ships around sector 12." She paused. "Wait. Isn't that where the shipyard is?"

"Yes it is." Said Anakin, his voice growing quiet. Both Ahsoka and Anakin's eyes widened as they both realized what had happened. The enemy knew they were going to attack the shipyards and waited in ambush for the main Republic fleet.

Anakin turned and said to the navigations officer "Set a course to the shipyards, as fast as we can! _I'm not going to let them fall into a trap_, he thought, _at least not without me._ Try to get in touch with Master Kenobi. Maybe we can warn him before it's too late."

Ahsoka punched in the comm, but all she got was a loud crackle of static. "Our communications are being jammed!"

"How? There aren't any ships near enough to block our signal." Anakin exclaimed. He turned to look out the viewport to find the source of the jamming. The three cruisers were passing over the asteroid belt when Anakin noticed something. One of the asteroids started glowing with lights. Then it started moving. "Over to the port! A Banking Clan Frigate!" As he said that, the prow turbolaser of the frigate fired and impacted on the shields of the _Firebird_ causing minimal damage, but shook the ship. Then all hell broke loose.

On board the CIS frigate, droids were manning their stations with rapt attention. The tactics of their captain were beyond their processor's ability to fully grasp, but they executed the orders quickly and without question. The captain had a violent dislike for slow battle droids. If any of those were found in his ranks, they tended to disappear and be replaced. And those were quickly replaced and similarly discarded if they in turn failed. A Super tactical droid, designated RW-47, with red trimmings stood watch over these droids, supervising them and checking their work. "There are three Republic ships. The right number that we need for your plan to work, my lord." It said in a heavy mechanical voice.

"Yes it is RW." A voice coming from the commander's chair hissed. "Now, execute phase two. Destroy one ship, damage another, and capture the final one. Just like how I planed out. "

"Yes sir." RW turned to the communications droid and told it, "Tell the boarding craft and the fighters to take off and follow their flight plans."

"Rodger Rodger." The droid said. RW looked out the viewport at the three Republic ships. Droid fighters and boarding craft took off from their positions in the asteroids and headed for the ships, following their instructions.

"Sir!" called the clone navigation officer as his screen started glowing with red, "Multiple contacts closing fast!" As the officer spoke a wing of Vulture droids flew past escorting a trio of boarding craft headed to the _Adamant_. Just then, an impact shook the _Dauntless _and forced the bridge crew to grab hold of something for balance. Vulture droids, now swarming en-masse were firing on the _Dauntless_, inflicting damage and lowering shield strength. Just then, the CIS frigate fired another salvo at the _Firebird_, this time blowing a chunk out of the bow armor of the ship.

Anakin hit the communications to all ships, "All Republic crews, launch all fighters, repeat, launch all fighters!" He watched as the ships responded and the _Venator_ Class Star Destroyers started to open their trademark dorsal flight deck doors. ARC-170's and V-wings departed from the fight deck. Over half of the first waves were picked off by Vulture droids and Tri-fighters, but the survivors managed to take off and engage the droids, creating a window for the next waves of fighters to get into position. A fierce dogfight soon raged out in space with both sides exchanging fire.

However, as the _Firebird_ was about to launch its third wave of fighters, an impact from a squad of crashing Tri-fighters momentarily weakened the shields surrounding the flight deck. Before the ship could re-route power, the CIS frigate fired directly into the ship, blowing a hole clean through the _Firebird's _flight deck and several other decks. As power flickered throughout the ship, an entire wing of Vulture droids changed course and flew directly into the bridge of the _Firebird_, destroying everyone in that section. The ship gave one last spasm and all power died. The CIS frigate then fired on the _Firebird_ for a fourth time and destroyed it, cutting the Republic's fleet power down by a third. Anakin and Ahsoka watched with horror as the ship turned into a fireball, killing everyone on board.

"Turbolaser crews, target the frigate!" Anakin ordered and a volley of blasts hit the frigate. "Where did all those fighters come from?"

"I don't know sir." Replied one of the clone commanders. "We were passing over the asteroid field when they suddenly were on us."

"They must have used the asteroids as cover and attacked when we were close enough." Anakin said. He had made a tactical blunder, rushing into a fight that was not planed. And now the crew of the _Firebird_ was dead. Anakin mentally kicked himself for being so blind, but then he remembered Obi-Wan's lesson: "_Keep your mind in the here and now."_ Anakin, following his mentor's advice activated his communicator and said, "Odd Ball, do you copy? What's the situation out there?"

_"General Skywalker."_ The voice of the clone commander replied over the comm. _"We have a bit of a problem, sir. A group of landing craft are attempting to board the Adamant. We shot two ships down, but more slipped in and we're getting hammered out here. Give us a few minuets then we can gain the upper hand."_

"Very well. Skywalker out." Anakin put down his communicator. The bridge shook again as a squad of Tri-fighter missiles impacted on their rapidly deteriorating shields. Bright flashes of light lit up space when fighters were destroyed as the two sides fought. Fighters were blown into molecular atoms by stray laser blasts, and pilots scrambled to gain a better position behind the enemy.


	4. Chapter 3- The Battle is Joined

**Hey Readers, here is the third chapter in this story. This part basically sets up a big confrontation between the Separatist Commander and Anakin/Ahsoka that will be coming up soon. I'm thinking about uploading a chapter every other day because I'm impatient and want to get it out. I'm also working on getting a cover of the story, but it won't be up for a few chapters. Anyway early Happy Thanksgiving! Enjoy!**

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Back on the bridge of the CIS frigate, the captain watched the battle play out with a small smile playing across his face. Not only was this going exactly as he planned, but those ships were part of the Open Circle Fleet under the command of Skywalker and Kenobi. The odds were that one of them was on board one of those ships. _Hopefully not the one we just destroyed,_ he thought, _because that would be a shame, to die so pitifully. _As the battle progressed, he recalled how those ships charged into his trap so easily. _So blinded they were to help the rest of their fleet, they ignored what was around them. It has to be Skywalker commanding these ships and Kenobi with the rest of the fleet. And with my plan, I'm bound to run into Skywalker._ That thought gave the commander a grin as he stroked the weapons on his belt. _Skywalker… the Chosen One. With such power he had the potential to be a great Sith if it weren't for the Jedi. _He paused as another thought crossed his mind. _Perhaps he still can be. _

RW-47 came over to him. "My lord, scans of the Republic's comm channels have confirmed that General Skywalker is onboard the Republic ship."

"Yes I know." The captain said with impatience. "Why do you think they charged right into our trap? Skywalker is impulsive, reckless, but above all, he values the lives under his command. Not your typical Jedi to say the least about him." He leaned back in his chair, the hood still covering his face. "General Skywalker is not your concern. Leave him to me." The frigate shook as a direct hit pierced part of their shields. The commander growled. CIS frigates were plentiful and great in large numbers, but a single ship cannot stand up to two Republic ships at once. He was taking a gamble, but he needed all of the ships in the sector to counter the Republic fleet at the shipyards, and with his strategies, the battle would soon turn in his favor. Then he could turn to other pressing agendas.

The _Dauntless_ and the _Adamant_ were trading fire with the lone CIS frigate. Now without the element of surprise, the battle was shifting in favor to the Republic as the _Venator_ class ships proved their superior firepower against the Banking Clan frigate. More and more ARC fighters were surviving the fierce dogfight as the number of droid fighters began to diminish, the clones proving once again that they are superior pilots to droids. Ahsoka was hard at work relaying and listening to the comm chatter amongst the fight. Anakin was coordinating the battle, giving orders and making sure his ship stayed intact. Just then, the lights over on the _Adamant_ flickered and the engines shut down. Ahsoka then received an emergency message from the captain of the _Adamant_.

"Master," she called to Anakin, "the _Adamant_ just lost power. Boarding parties have succeeded in cutting main power to the _Adamant_ and now she's operating on emergency battery power. They need a few minutes to repair their systems."

"They might not have a few minutes." Anakin said. "Look." Outside, the CIS frigate had started to head to the _Adamant_, firing its prow turbolaser at it. The ship would not be able to take much more of the fire; already chunks of the _Adamant's_ armor were being blasted off. What saved it from the same fate as the _Firebird_ was that their hanger doors were closed having launched all their fighters. But that would only protect them for so long. "Move us between the frigate and the _Adamant_." Anakin ordered. "We should be able to draw its fire to protect the _Adamant_ for now." The _Dauntless_ moved forward, continuously firing at the frigate. Strangely, the CIS frigate had not fired back, only targeting the _Adamant_ and the fighters around both ships, completely ignoring the _Dauntless_.

By now the _Dauntless_ had almost moved between the two ships, and a large portion of the Confederate fighters had been eliminated. "This battle is almost over." He told Ahsoka as he moved next to her. "Keep trying to get in touch with Obi-wan. We need to warn him before he arrives in the trap."

"I'll say this, the Separatists seem to finally have a competent military leader." Ahsoka smirked. "They used the same trick you did by hiding their ship and their fighters in the asteroids to avoid detection."

"Yes, I know. Whoever he is must have read up on past battles and is a seasoned strategist." Anakin admitted. "The commander is probably the one who has designed those victories for the Confederacy recently."

The comm hissed and Ahsoka exclaimed, "I've got a signal! It's weak though, so make it brief."

Anakin turned to the holo projectors and a garbled picture of Kenobi appeared. "Obi-wan, the Confederate fleet is not orbiting the planet. They're all protecting the shipyard. You're flying into a trap!"

_"Say again Anakin, your transm-… unclear."_ Obi-wan said, interrupted by a burst of static.

"You're flying into a trap, master!" Anakin shouted. Halfway through his sentence, the image of Kenobi disappeared entirely. Anakin looked up just as the entire bridge crew gasped in alarm. The CIS frigate, which was heading toward the _Adamant_, was suddenly extremely close to the _Dauntless_ having performed an amazing ninety-degree turn in just a few seconds. Collision alarms sounded due to the close proximity of the frigate. Having pulled up next to the _Dauntless_, the frigate then extended its boarding port, cutting through the hull of the Republic ship. Collision alarms quickly changed tone as the intruder alarm sounded, and messages of droids onboard started flooding in.

Anakin turned and stared to run out of the bridge. "Come on Ahsoka!" He said as the doors parted and he ran through. Ahsoka was only too happy to oblige, running after her master to confront the droids.

RW-47 had moved down with the boarding parties to coordinate their attack. The goal was to kill every last Republic officer on both ships, starting with this one. They would then pilot the ships into the shipyard battle and obliterate the Republic fleet in a surprise attack. Since the frigate and the Republic ship were currently so close together, they could not fire on each other without risk of damaging themselves. This same reason was also what prevented the fighters from firing on either ship. Once takeover was complete, the captain would disembark and assume control over this Republic ship. The order would be given to the Republic fighters to dock in their home vessel, and then the droids awaiting them would slaughter them, preventing anyone from giving away the attack. Then they would destroy their own frigate to give the assumption that the Republic forces won the battle. Another attack force would take over the other Republic ship and they would head into the space battle.

As the boarding door opened, RW-47 noted the intense fire that greeted them. The first wave of droids and most of the second were wiped out. But the third and consecutive groups sustained less and less casualties as they forced the clones back. "Soon this ship will be ours." RW said. The droids around it gave off identical "Rodger Rodger's" which then proceeded to spread around like a wave among the other droids. RW gave off a passible vocalization of an organic sigh before marching on board the Republic ship.

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**What do you think will happen next? Which side will get the better of the other? You'll find out soon!**


	5. Chapter 4- Change of Pace

**Hey readers! I couldn't resist uploading another chapter today, so here it is. I'm just about to go to a friend's for Thanksgiving so I'm frantically trying to get this up before I go. Anyway, enjoy your food!**

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"So what's the plan master?" Ahsoka said as the two Jedi raced through the corridors of the _Dauntless_ to the docking port. Clone troopers were barely able to contain the droids as they poured in, and would not be able to hold the line for long. Already isolated squads of droids had been detected on other decks and were being countered.

"Our plan is to fight our way through the droids and find the commander of that ship. Then we decide from there." Anakin responded. Ahsoka nodded, knowing that they had two choices at that juncture: either capture the commander or kill him. As a Jedi it is wrong to kill unarmed opponents, but some situations in battle don't allow for that option. This is were the Jedi walk the thin line between heroes and war criminals, those split second decisions on the battlefield.

As the two went on the sounds of blaster fire got louder until they rounded a corner and ran right into a fire fight between clones and droids. The droids were taking casualties but they were still advancing through sheer numbers. However this all changed when Anakin and Ahsoka showed up. Without missing a beat, both of them activated their lightsabers: Anakin with his single blue lightsaber and Ahsoka with her normal green lightsaber and a smaller yellow-green shoto, both held in the Shien reverse grip. Charging right into the center of the droids, deflecting blasts with their lightsabers back into the droids that fired them, the two Jedi made short work of those droids.

After vertically slicing the last droid from the top-down, Anakin went over to the leader of these clones, Captain Rex. "How bad is it Rex?"

"It's pretty bad, sir." The clone answered as he holstered his pistols. "From what I've heard, the droids are starting to push past our defenses and are spreading out all over the ship. They've practically taken over the docking port. There are still a few men down there including ARC trooper Fives, but their position is vulnerable to a full on attack."

Anakin hurriedly turned from Rex. "I'm going down there to help our men. After that, I'm going to board that frigate and see just whom we are dealing with. Round up as many men as you can. Our rally point will be in the docking port. Understand?"

Rex snapped to attention. "Yes sir!"

"Very good. Come on Ahsoka, we still got plenty of work left to do."

"Happy to oblige." She said with a smile. Anakin gave a small smile of his own and they both started for the docking bay along with Rex and his company.

The droids had forced the clones in the docking bay to retreat, and more droids were coming onboard when RW's internal transmitter was signaled. "What is it?" RW asked.

A battle droid commander's vocalizer responded, "Sir, two Jedi are making their way to your position. We can't stop them." The transmission was cut of with the sound of the droid screaming and the hum of a lightsaber.

Before RW could respond the captain's voice came over all droid frequencies, _"This is the captain. All droids are to avoid direct contact with the Jedi. Instead, let them board the ship and lead them to me. Eliminate any stragglers they bring."_ His voice cut off.

"You heard the captain," RW-47 said to the droids around him, "vacate the area. The Jedi are logically going to try to board from this point." The droids heeded its orders and either moved deeper into the Republic ship or back onto their own ship, whichever was closer. RW remained on the Republic ship to continue the captain's previous orders. As the droid moved, there was a change of pitch in the battle as a humming sound entered his audio receptors. Recognizing that sound as that of a lightsaber, RW quickly made his exit deeper into the Republic ship.

Several corridors and piles of wrecked droids later, Anakin and Ahsoka rushed into the docking bay. Behind them was a group of about thirty clones that they had rounded up from various fights, about two battle groups worth. The decks of the _Dauntless _were swarming with battle droids and it was taking everything the crew had to offer to hold them back. It was estimated that there were over several thousand droids onboard and all personal were assigned to combat duty. Anakin and Ahsoka managed to cut down the number of droids and had rescued several fire teams that were close to being overrun. Now the _Dauntless_ was putting up more of a resistance against the droids, but there was still a long ways to go before an outcome could be determined.

But as they entered the docking bay, only the bodies of dead clones and destroyed droids greeted them instead of the blaster fire they expected. After a quick scan Ahsoka spotted a group of droids exiting through a door on their far left. "Look! Over there, a Super tactical droid!"_ If we could capture it_, she thought, _we could learn about the Separatists' plans and turn them against them. _

Anakin had he same thought. "Rex, take these men and capture that tactical droid. It may hold the key to stopping the Separatists."

"On it sir." He replied. "Come on!" he motioned to the troopers and they set off in pursuit of the droids. They quickly got to the door and entered leaving the two Jedi alone.

"Now it's our turn." Anakin said to Ahsoka. As they walked to the boarding ramp, a side door opened. Both of them shifted their lightsabers in preparation for an attack, but instead of droids, it was a group of clones.

"General Skywalker, Commander Tano." The clone called Fives said. "We didn't hear any noise coming from here, so we thought we try to re-establish our position before more droids showed up." He pointed to a once elaborate barricade that was now pretty beat up.

"Looks like you were down here since the fight started." Ahsoka said.

"Yes sir. We had one hell of a fight."

"Good job Fives." Anakin said to the ARC trooper. "Now I want you to take these troopers and go through that door over there." He said pointing to the door Rex just went through. "You'll meet up with Captain Rex who is pursuing a Super tactical droid. I think he may need your help."

Fives nodded. "Always happy to blast some droids sir." He said, and then started off towards the door with the rest of the clones behind him.

"Let's go master. We have a commander to catch." Ahsoka said.

Anakin nodded his head and they resumed boarding the CIS frigate.

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**Cover coming soon! Until then, what will they find onboard?**


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